Ian and Barbara awaken after being knocked unconscious by the turbulence. Clearly suffering from sort of amnesia, and acting very strangely, they try to make sense of their surroundings. When Susan comes to, she acts even more bizarrely, going so far as to threaten to stab Ian with a pair of scissors, and being unable to touch the console without experiencing pain. The doors to the ship open and close of their own accord while the TARDIS is in flight, and the scanner begins to show the travellers images of danger.
The Doctor awakens, suffering from a head wound, and immediately is suspicious of Ian and Barbara. He accuses them of sabotaging the ship deliberately, and threatens to throw them off. Barbara, the only one that seems to be coming to her senses, tries to calm everyone and convince them that they are in danger.
The Doctor discovers that a piece of equipment called the Fast Return Switch is malfunctioning, and it's forcing the ship back to the creation of the universe, and to its own destruction. The strange disturbances and their bizarre behaviour is the result of the TARDIS attempting to warn them of the danger. The Doctor repairs the switch, saving them all, and the experience has caused him to finally accept Ian and Barbara; he apologizes to them, and the travellers are finally becoming friends.
The TARDIS materializes on a snowy mountainside, and the women find a massive footprint in the snow.
One area where this serial does succeed is in helping the travelers finally pull together and get past any mistrust and suspicion that still lingered from the pilot episode. After this story, the crew would be far more united than they had been. Even though this resulted in the Doctor's character growing less complicated and more straightforwardly heroic, I'm of the opinion that it was necessary to allow the character to take on more of an active role, and be less of an obstruction.
So, while the story itself is mostly nonsense, it does accomplish something of value. This is also the first time the TARDIS is insinuated to be alive, a fact that surprises even the Doctor.